AltSci Cell

You may have been patiently waiting for the first installment of my nanotechnology blog and you're right to expect great things. I have found myself pushing more and more stuff onto my stack and there will be a time for popping all those off the stack. The first one is what I've been working on the past three weeks.

There are plenty of tutorials for GROMACS but because I had a bunch of problems using it, I thought I would write another one. My tutorial is based on this one, so if you want the original, look there.

First, we need a molecule to minimize*. We could use 1OEI, but let's start with a blank slate. Minimizing an already minimized protein is kinda boring.

PyMOL allows you to create proteins from scratch. Use the builder to create a simple two-residue peptide, acetyl-alanine. You can do this by clicking Builder, then Protein, then Ace, then Create As New Object. Then simply click Ala. You can also do this with two lines of Python pasted directly into the command prompt:

At this point we can obviously see that we should have more steps. Potential energy went from 337 kJ/mol to 5 kJ/mol in 25 steps. Therefore, another 25 steps would be worthwhile. Let's try with 100 steps. em100.mdp now says steps = 100

PyMOL is a very complex program which can do an impressive list of things. I won't get into exactly what you can do with it, but believe me it's extensive. The protein creation we did at the beginning was just one piece of it's code.

It turns out that the minimization converges at 166 steps, so it's not too far away from done. The potential energy it settles down into is -17.5 kJ/mol, only 5 more units than what we had. Surprising though is that the difference in the two models is very small.

If you want to look at the trajectory, try this:

trjconv -f traj.trr -o aceala1_trj.pdb

It will ask for the group. Group 0 is everything, so pick it.

The next step in our journey is to scale up our operations. Instead of making a two-item protein, let's minimize a real protein.

I picked a random one, 1OEI and downloaded the pdb. You're welcome to look for a different protein but many proteins use modified residues, so they will cause GROMACS to throw errors. For example, I wanted to minimize 3RJV because it is currently being studied by Fold.it. It turns out that it uses a modified residue, MSE. MSE contains selenium, which is a fairly interesting semiconductor. MSE can be found in Brazil nuts, cereal grains, soybeans, and grassland legumes according to Wikipedia.

So let's minimize our real protein.

Since GROMACS has many default files that we'll be using, it makes sense to create a directory and work in it for the duration of your work. I use just one non-default file and the reason for that is just habit.

If you run this: pdb2gmx -f 1OEI.pdb -o 1OEI.gro
you will get an error complaining about:
"Atom HB3 in residue HIS 61 was not found in rtp entry NHID with 19 atoms
while sorting atoms."

This is because the naming of atoms in residues is not completely standardized. Therefore hydrogens are often incorrectly named in PDB files. GROMACS has a flag to solve that called "-ignh". It ignores hydrogens when trying to figure out what is connected to what. Since hydrogens can only have one bond, they are always only connected to one thing, so they can be safely ignored most of the time.

It finished very quickly in just 25 steps. It ended up with potential energy of -386 kJ/mol. Of course this file has already been minimized. If you look at the input file in PyMOL, you will notice that there are 20 models, GROMACS only worked on the first. If you're interested, try minimizing the others. You might have noticed the warning in the output "Energy minimization has stopped, but the forces have not converged to the requested precision Fmax < 100 (which may not be possible for your system)." This means that the forces are higher than we want them to be. In this case, they're 1836 kJ mol-1 nm-1. This is a lot higher than we intended, but that's okay since we successfully minimized it.

Below you can see my rendering as a cartoon. Of course proteins can be rendered in multiple ways, ball and stick gives you a slightly more accurate rendering while the cartoon gives you an overview of the structure.

This concludes the tutorial. In this tutorial we

Created a peptide with PyMOL.

Minimized it with GROMACS.

Downloaded a real protein.

Minimized it with GROMACS.

To minimize the protein, we used practically the same commands which generalizes the concept. Where do we go from here? 3RJV would be a wonderful molecule to attempt to minimize. This requires Amber force fields for MSE and possibly other residues. AmberTools14 is available under open source licenses but requires registration. Amber is a very expensive commmercial product. Another way to create a topology for 3RJV would be to use g_x2top. It is a rough tool but may work. Another goal would be to learn other commands from GROMACS. GROMACS contains a large number of commands and functionality. For example, GROMACS supports GPU acceleration. Testing that with a difficult non-optimized molecule would be a good test. Finding a protein that is improperly minimized and minimizing it would be a worthwhile goal. This may require downloading all files from WWPDB or may be as simple as browsing RCSB PDB. The new X-ray validation reports are worthwhile to find problematic proteins.

Most people ask how it's going. It's difficult and fun. I expected it to be difficult and I've spent a lot of time in the past 3.5 months doing things that are not directly related to nanotechnology. But I've had fun doing nanotech and I've had fun doing other stuff.

I attended a seminar series at the University of Washington's Molecular Engineering and Sciences Institute. The next one starts at the end of September if you're interested in attending.

I finished reading Nanosystems and compiled a list of things to ask Dr. K. Eric Drexler. A full book report will follow in the future.

Before I go I'd like to invite hackers amongst my readers to come to Neg9 Seattle Summer Hack Fest on July 3, 2014. It will not focus on nanotech nor talking, just hacking. If I don't write before Friday, have a wonderful Independence Day. This year I'm celebrating independence from a 9-to-5 job.

Comments: 6

I see you don't monetize your site, don't waste your traffic, you can earn extra cash every month because you've got hi quality content. If you want to know how to make extra bucks, search for: Mrdalekjd methods for $$$

I just could nott leave your website prior to sugggesting that I actually loved the usual information a person supply on your visitors?Is going to be again frequently in orer to check up on new postsbeasisxwa teknik mesin

I'm really loving the theme/design of your weblog.Do you ever run into any browser compatibility problems?A handful of my blog visitors have complained about my website not operating correctly in Explorer but looks great in Safari.Do you have any solutions to help fix this problem?

Leave a Reply

Your Name

Name *

Email *

Website

If you enter anything in this field your comment will be treated as spam: